| Previous changeset 0:9959fa526f1a (2016-04-20) Next changeset 2:05766022dfc4 (2020-09-14) |
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Commit message:
planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit 9fcfd73aaf19aa65e2087ae003998f21971b6f9b-dirty |
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modified:
compare_humann2_output.xml |
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added:
test-data/more_abundant_pathways.tabular test-data/sample_1_pathway_abundances.tabular test-data/sample_1_specific_pathways.txt test-data/sample_2_pathway_abundances.tabular test-data/sample_2_specific_pathways.txt test-data/sample_comparison_log.txt test-data/sample_similar_pathways.tabular |
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removed:
test-data/humann2_fasta_pathabundance_relab_renormalized.csv test-data/humann2_m8_pathabundance_cmp_renormalized.tsv test-data/log_output.txt test-data/more_abundant_output.tabular test-data/similar_output.tabular test-data/specific_to_sample1_output.txt test-data/specific_to_sample2_output.txt |
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| diff -r 9959fa526f1a -r c1aca37cb1fc compare_humann2_output.xml --- a/compare_humann2_output.xml Wed Apr 20 08:30:08 2016 -0400 +++ b/compare_humann2_output.xml Wed Apr 20 09:15:27 2016 -0400 |
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| @@ -1,5 +1,5 @@ <tool id="compare_humann2_output" name="Compare outputs of HUMAnN2 for several samples" version="0.1.0"> - <description>and extract information</description> + <description>and extract similar and specific information</description> <requirements> </requirements> @@ -54,16 +54,16 @@ <tests> <test> <param name="samples_0|sample_name" value="sample1"/> - <param name="samples_0|input" value="humann2_m8_pathabundance_cmp_renormalized.tsv"/> + <param name="samples_0|input" value="sample_1_pathway_abundances.tabular"/> <param name="samples_1|sample_name" value="sample2"/> - <param name="samples_1|input" value="humann2_fasta_pathabundance_relab_renormalized.csv"/> + <param name="samples_1|input" value="sample_2_pathway_abundances.tabular"/> <param name="charact_nb" value="10"/> - <output name="more_abundant_output_file" file="more_abundant_output.tabular"/> - <output name="similar_output_file" file="similar_output.tabular"/> - <output name="log" file="log_output.txt"/> + <output name="more_abundant_output_file" file="more_abundant_pathways.tabular"/> + <output name="similar_output_file" file="sample_similar_pathways.tabular"/> + <output name="log" file="sample_comparison_log.txt"/> <output_collection name="specific_files" type="list"> - <element name="specific_to_sample1" file="specific_to_sample1_output.txt" /> - <element name="specific_to_sample2" file="specific_to_sample2_output.txt" /> + <element name="specific_to_sample1" file="sample_1_specific_pathways.txt" /> + <element name="specific_to_sample2" file="sample_2_specific_pathways.txt" /> </output_collection> </test> </tests> @@ -76,7 +76,7 @@ * Similar gene families or pathways between the samples and the relative abundances of these similar characteristics * Most abundant gene families or pathways for each sample and the corresponding relative abundance in all samples - + * Specific gene families and pathways for each samples and the relative abundances of these specific characteristics ]]></help> |
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| diff -r 9959fa526f1a -r c1aca37cb1fc test-data/humann2_fasta_pathabundance_relab_renormalized.csv --- a/test-data/humann2_fasta_pathabundance_relab_renormalized.csv Wed Apr 20 08:30:08 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b"@@ -1,267 +0,0 @@\n-# Pathway\thumann2_Abundance\n-PYRIDOXSYN-PWY: pyridoxal 5'-phosphate biosynthesis I\t0.0245442\n-PYRIDOXSYN-PWY: pyridoxal 5'-phosphate biosynthesis I|unclassified\t0.0341296\n-PWY-3841: folate transformations II\t0.0238544\n-PWY-3841: folate transformations II|unclassified\t0.0227477\n-1CMET2-PWY: N10-formyl-tetrahydrofolate biosynthesis\t0.0212689\n-1CMET2-PWY: N10-formyl-tetrahydrofolate biosynthesis|unclassified\t0.00834716\n-PWY-7208: superpathway of pyrimidine nucleobases salvage\t0.0206908\n-PWY-7208: superpathway of pyrimidine nucleobases salvage|unclassified\t0.0175918\n-COA-PWY-1: coenzyme A biosynthesis II (mammalian)\t0.019437\n-PWY-7221: guanosine ribonucleotides de novo biosynthesis\t0.0188123\n-CALVIN-PWY: Calvin-Benson-Bassham cycle\t0.0179034\n-CALVIN-PWY: Calvin-Benson-Bassham cycle|unclassified\t0.0240344\n-PWY66-422: D-galactose degradation V (Leloir pathway)\t0.0175745\n-PWY66-422: D-galactose degradation V (Leloir pathway)|g__Bacteroides.s__Bacteroides_stercoris\t0.0149592\n-PWY66-422: D-galactose degradation V (Leloir pathway)|unclassified\t0.0104266\n-PWY-1042: glycolysis IV (plant cytosol)\t0.0175553\n-PWY-1042: glycolysis IV (plant cytosol)|unclassified\t0.0193529\n-PWY-5100: pyruvate fermentation to acetate and lactate II\t0.0170667\n-PWY-5100: pyruvate fermentation to acetate and lactate II|unclassified\t0.0126625\n-DTDPRHAMSYN-PWY: dTDP-L-rhamnose biosynthesis I\t0.0169441\n-DTDPRHAMSYN-PWY: dTDP-L-rhamnose biosynthesis I|unclassified\t0.0250835\n-PWY-7228: superpathway of guanosine nucleotides de novo biosynthesis I\t0.0169262\n-HOMOSER-METSYN-PWY: L-methionine biosynthesis I\t0.0158217\n-HOMOSER-METSYN-PWY: L-methionine biosynthesis I|unclassified\t0.0109381\n-PWY-7219: adenosine ribonucleotides de novo biosynthesis\t0.0157923\n-PWY-7219: adenosine ribonucleotides de novo biosynthesis|unclassified\t0.0333171\n-PWY-7229: superpathway of adenosine nucleotides de novo biosynthesis I\t0.0155872\n-PWY-7229: superpathway of adenosine nucleotides de novo biosynthesis I|unclassified\t0.0261337\n-PWY-6125: superpathway of guanosine nucleotides de novo biosynthesis II\t0.0155645\n-PWY-5505: L-glutamate and L-glutamine biosynthesis\t0.0153682\n-PWY-5505: L-glutamate and L-glutamine biosynthesis|unclassified\t0.0196045\n-PWY-5505: L-glutamate and L-glutamine biosynthesis|g__Bacteroides.s__Bacteroides_thetaiotaomicron\t0.0144739\n-PWY-6126: superpathway of adenosine nucleotides de novo biosynthesis II\t0.0150984\n-PWY-6126: superpathway of adenosine nucleotides de novo biosynthesis II|unclassified\t0.0244065\n-PWY-7220: adenosine deoxyribonucleotides de novo biosynthesis II\t0.0148474\n-PWY-7220: adenosine deoxyribonucleotides de novo biosynthesis II|unclassified\t0.0201368\n-PWY-7222: guanosine deoxyribonucleotides de novo biosynthesis II\t0.0148474\n-PWY-7222: guanosine deoxyribonucleotides de novo biosynthesis II|unclassified\t0.0201368\n-PWY-6703: preQ0 biosynthesis\t0.0139768\n-PWY-6703: preQ0 biosynthesis|unclassified\t0.013368\n-PWY-5659: GDP-mannose biosynthesis\t0.013223\n-PWY-5659: GDP-mannose biosynthesis|unclassified\t0.00106616\n-SER-GLYSYN-PWY: superpathway of L-serine and glycine biosynthesis I\t0.012955\n-SER-GLYSYN-PWY: superpathway of L-serine and glycine biosynthesis I|unclassified\t0.00288758\n-ILEUSYN-PWY: L-isoleucine biosynthesis I (from threonine)\t0.0129401\n-ILEUSYN-PWY: L-isoleucine biosynthesis I (from threonine)|unclassified\t0.0159474\n-VALSYN-PWY: L-valine biosynthesis\t0.0129401\n-VALSYN-PWY: L-valine biosynthesis|unclassified\t0.0159474\n-PWY-6936: seleno-amino acid biosynthesis\t0.012799\n-PWY-6936: seleno-amino acid biosynthesis|unclassified\t0.0132349\n-PWY-5030: L-histidine degradation III\t0.0122713\n-PWY-5030: L-histidine degradation III|unclassified\t0.0120381\n-HSERMETANA-PWY: L-methionine biosynthesis III\t0.0121379\n-HSERMETANA-PWY: L-methionine biosynthesis III|unclassified\t0.00515875\n-PWY0-162: superpathway of pyrimidine ribonucleotides de novo biosynthesis\t0.0119161\n-PWY0-162: superpathway of pyrimidine ribonucleotides de novo biosynthesis|unclassif"..b"ryotes)\t0.00104748\n-PWY-5754: 4-hydroxybenzoate biosynthesis I (eukaryotes)|unclassified\t0.00229464\n-P185-PWY: formaldehyde assimilation III (dihydroxyacetone cycle)\t0.00103843\n-P185-PWY: formaldehyde assimilation III (dihydroxyacetone cycle)|unclassified\t0.00115303\n-PWY-6595: superpathway of guanosine nucleotides degradation (plants)\t0.00102956\n-PWY-6595: superpathway of guanosine nucleotides degradation (plants)|unclassified\t0.00225538\n-PWY-5464: superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle\t0.000992505\n-PWY-5464: superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle|unclassified\t0.00172005\n-THISYNARA-PWY: superpathway of thiamin diphosphate biosynthesis III (eukaryotes)\t0.000973654\n-THISYNARA-PWY: superpathway of thiamin diphosphate biosynthesis III (eukaryotes)|unclassified\t0.0021303\n-PWY-6386: UDP-N-acetylmuramoyl-pentapeptide biosynthesis II (lysine-containing)\t0.000904748\n-PWY-6386: UDP-N-acetylmuramoyl-pentapeptide biosynthesis II (lysine-containing)|unclassified\t0.00183333\n-THRESYN-PWY: superpathway of L-threonine biosynthesis\t0.000904039\n-THRESYN-PWY: superpathway of L-threonine biosynthesis|unclassified\t0.00188356\n-PWY0-1586: peptidoglycan maturation (meso-diaminopimelate containing)\t0.000751931\n-PWY0-1586: peptidoglycan maturation (meso-diaminopimelate containing)|unclassified\t0.0014413\n-FAO-PWY: fatty acid β-oxidation I\t0.000714249\n-FAO-PWY: fatty acid β-oxidation I|unclassified\t0.00148771\n-PWY-5136: fatty acid β-oxidation II (peroxisome)\t0.000698245\n-PWY-5136: fatty acid β-oxidation II (peroxisome)|unclassified\t0.00144209\n-PWY-6471: peptidoglycan biosynthesis IV (Enterococcus faecium)\t0.000698193\n-PWY-6471: peptidoglycan biosynthesis IV (Enterococcus faecium)|unclassified\t0.00142191\n-PWY-7007: methyl ketone biosynthesis\t0.000659038\n-PWY-7007: methyl ketone biosynthesis|unclassified\t0.00122854\n-GLCMANNANAUT-PWY: superpathway of N-acetylglucosamine, N-acetylmannosamine and N-acetylneuraminate degradation\t0.000651572\n-GLCMANNANAUT-PWY: superpathway of N-acetylglucosamine, N-acetylmannosamine and N-acetylneuraminate degradation|unclassified\t0.00123299\n-PWY-6769: rhamnogalacturonan type I degradation I (fungi)\t0.000634893\n-PWY-6769: rhamnogalacturonan type I degradation I (fungi)|unclassified\t0.00139081\n-PWY-6309: L-tryptophan degradation XI (mammalian, via kynurenine)\t0.000615914\n-PWY-6309: L-tryptophan degradation XI (mammalian, via kynurenine)|unclassified\t0.00134924\n-PWY-7094: fatty acid salvage\t0.000597229\n-PWY-7094: fatty acid salvage|unclassified\t0.00125407\n-GLUDEG-I-PWY: GABA shunt\t0.000537709\n-GLUDEG-I-PWY: GABA shunt|unclassified\t0.001173\n-PWY1F-823: leucopelargonidin and leucocyanidin biosynthesis\t0.000501896\n-PWY1F-823: leucopelargonidin and leucocyanidin biosynthesis|unclassified\t0.00109947\n-PWY-7234: inosine-5'-phosphate biosynthesis III\t0.00045368\n-PWY-7234: inosine-5'-phosphate biosynthesis III|unclassified\t0.000993843\n-PWY-5173: superpathway of acetyl-CoA biosynthesis\t0.000372086\n-PWY-5173: superpathway of acetyl-CoA biosynthesis|unclassified\t0.000785602\n-PWY-6731: starch degradation III\t0.000336222\n-PWY-6731: starch degradation III|unclassified\t0.000708616\n-P241-PWY: coenzyme B biosynthesis\t0.000322755\n-P241-PWY: coenzyme B biosynthesis|unclassified\t0.000707035\n-PWY-7398: coumarins biosynthesis (engineered)\t0.000273932\n-PWY-7398: coumarins biosynthesis (engineered)|unclassified\t0.000600083\n-PWY-4041: γ-glutamyl cycle\t0.000269421\n-PWY-4041: γ-glutamyl cycle|unclassified\t0.000590201\n-GLYOXYLATE-BYPASS: glyoxylate cycle\t0.000182141\n-GLYOXYLATE-BYPASS: glyoxylate cycle|unclassified\t0.000395503\n-GLYCOL-GLYOXDEG-PWY: superpathway of glycol metabolism and degradation\t0.000175574\n-GLYCOL-GLYOXDEG-PWY: superpathway of glycol metabolism and degradation|unclassified\t0.000384618\n-SO4ASSIM-PWY: sulfate reduction I (assimilatory)\t6.96955e-05\n-SO4ASSIM-PWY: sulfate reduction I (assimilatory)|unclassified\t0.00015138\n" |
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| diff -r 9959fa526f1a -r c1aca37cb1fc test-data/humann2_m8_pathabundance_cmp_renormalized.tsv --- a/test-data/humann2_m8_pathabundance_cmp_renormalized.tsv Wed Apr 20 08:30:08 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,17 +0,0 @@ -# Pathway humann2_Abundance -ARGININE-SYN4-PWY: L-ornithine de novo biosynthesis 353741 -ARGININE-SYN4-PWY: L-ornithine de novo biosynthesis|unclassified 353741 -HSERMETANA-PWY: L-methionine biosynthesis III 150089 -HSERMETANA-PWY: L-methionine biosynthesis III|unclassified 150089 -DTDPRHAMSYN-PWY: dTDP-L-rhamnose biosynthesis I 142538 -DTDPRHAMSYN-PWY: dTDP-L-rhamnose biosynthesis I|unclassified 142538 -KETOGLUCONMET-PWY: ketogluconate metabolism 96153.8 -KETOGLUCONMET-PWY: ketogluconate metabolism|unclassified 96153.8 -PWY-1269: CMP-3-deoxy-D-manno-octulosonate biosynthesis I 82608.9 -PWY-1269: CMP-3-deoxy-D-manno-octulosonate biosynthesis I|unclassified 82608.9 -PWY-7357: thiamin formation from pyrithiamine and oxythiamine (yeast) 72056.1 -PWY-7357: thiamin formation from pyrithiamine and oxythiamine (yeast)|unclassified 72056.1 -PWY-6151: S-adenosyl-L-methionine cycle I 69841.3 -PWY-6151: S-adenosyl-L-methionine cycle I|unclassified 69841.3 -PWY-6897: thiamin salvage II 32971.5 -PWY-6897: thiamin salvage II|unclassified 32971.5 |
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| diff -r 9959fa526f1a -r c1aca37cb1fc test-data/log_output.txt --- a/test-data/log_output.txt Wed Apr 20 08:30:08 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,12 +0,0 @@ -Similar between all samples: 15 -Specific to samples: - sample1 - All: 16 - Number of specific characteristics: 1 - Percentage of specific characteristics: 6.25 - Relative abundance of specific characteristics(%): 6984130.0 - sample2 - All: 266 - Number of specific characteristics: 251 - Percentage of specific characteristics: 94.3609022556 - Relative abundance of specific characteristics(%): 186.11689025 |
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| diff -r 9959fa526f1a -r c1aca37cb1fc test-data/more_abundant_output.tabular --- a/test-data/more_abundant_output.tabular Wed Apr 20 08:30:08 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,21 +0,0 @@ -id name sample1 sample2 -PWY-7208 superpathway of pyrimidine nucleobases salvage|unclassified 0 1.75918 -PWY-7208 superpathway of pyrimidine nucleobases salvage 0 2.06908 -PYRIDOXSYN-PWY pyridoxal 5 phosphate biosynthesis I 0 2.45442 -ARGININE-SYN4-PWY L ornithine de novo biosynthesis 35374100.0 0.809135 -PYRIDOXSYN-PWY pyridoxal 5 phosphate biosynthesis I|unclassified 0 3.41296 -HSERMETANA-PWY L methionine biosynthesis III|unclassified 15008900.0 0.515875 -DTDPRHAMSYN-PWY dTDP L rhamnose biosynthesis I 14253800.0 1.69441 -HSERMETANA-PWY L methionine biosynthesis III 15008900.0 1.21379 -DTDPRHAMSYN-PWY dTDP L rhamnose biosynthesis I|unclassified 14253800.0 2.50835 -PWY-3841 folate transformations II 0 2.38544 -ARGININE-SYN4-PWY L ornithine de novo biosynthesis|unclassified 35374100.0 1.66731 -1CMET2-PWY N10 formyl tetrahydrofolate biosynthesis 0 2.12689 -1CMET2-PWY N10 formyl tetrahydrofolate biosynthesis|unclassified 0 0.834716 -PWY-3841 folate transformations II|unclassified 0 2.27477 -PWY-1269 CMP 3 deoxy D manno octulosonate biosynthesis I 8260890.0 0.755658 -PWY-1269 CMP 3 deoxy D manno octulosonate biosynthesis I|unclassified 8260890.0 0.644897 -KETOGLUCONMET-PWY ketogluconate metabolism 9615380.0 0.141222 -KETOGLUCONMET-PWY ketogluconate metabolism|unclassified 9615380.0 0.309365 -COA-PWY-1 coenzyme A biosynthesis II 0 1.9437 -PWY-7221 guanosine ribonucleotides de novo biosynthesis 0 1.88123 |
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| diff -r 9959fa526f1a -r c1aca37cb1fc test-data/more_abundant_pathways.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/more_abundant_pathways.tabular Wed Apr 20 09:15:27 2016 -0400 |
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| @@ -0,0 +1,16 @@ +id name sample1 sample2 +PWY-3781 aerobic respiration I |g__Escherichia.s__Escherichia_coli 11428.460877 3504.59201375 +PWY-3781 aerobic respiration I |g__Neisseria.s__Neisseria_meningitidis 142.20887339 6845.43838944 +PWY-3781 aerobic respiration I |g__Staphylococcus.s__Staphylococcus_aureus 31496.0304037 2108.46546528 +PWY-3781 aerobic respiration I |g__Acinetobacter.s__Acinetobacter_baumannii 0 10661.254254 +PWY-3781 aerobic respiration I |g__Deinococcus.s__Deinococcus_radiodurans 243.95473535 51964.0681305 +PWY66-389 phytol degradation|g__Staphylococcus.s__Staphylococcus_aureus 31048.8482071 3743.72936189 +PWY-3781 aerobic respiration I |g__Helicobacter.s__Helicobacter_pylori 475.85206385 7486.51278743 +PWY66-389 phytol degradation 97948.0570109 126799.82205 +PWY-3781 aerobic respiration I |unclassified 3699.62755214 1118.9863796 +PWY-3781 aerobic respiration I |g__Actinomyces.s__Actinomyces_odontolyticus 0 2772.58262062 +PWY-3781 aerobic respiration I |g__Pseudomonas.s__Pseudomonas_aeruginosa 7491.56572789 2317.68361723 +PWY-3781 aerobic respiration I |g__Rhodobacter.s__Rhodobacter_sphaeroides 45855.0506957 7356.87095282 +PWY-3781 aerobic respiration I |g__Staphylococcus.s__Staphylococcus_epidermidis 29048.5287092 8522.11671136 +PWY-3781 aerobic respiration I |g__Propionibacterium.s__Propionibacterium_acnes 307.60781448 14416.0404018 +PWY-3781 aerobic respiration I 146949.349575 137931.175616 |
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| diff -r 9959fa526f1a -r c1aca37cb1fc test-data/sample_1_pathway_abundances.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample_1_pathway_abundances.tabular Wed Apr 20 09:15:27 2016 -0400 |
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| b'@@ -0,0 +1,2313 @@\n+# Pathway\thumann2_Abundance\n+PWY-3781: aerobic respiration I (cytochrome c)\t1469.4934957509\n+PWY-3781: aerobic respiration I (cytochrome c)|g__Rhodobacter.s__Rhodobacter_sphaeroides\t458.5505069573\n+PWY-3781: aerobic respiration I (cytochrome c)|g__Staphylococcus.s__Staphylococcus_aureus\t314.9603040367\n+PWY-3781: aerobic respiration I (cytochrome c)|g__Staphylococcus.s__Staphylococcus_epidermidis\t290.4852870919\n+PWY-3781: aerobic respiration I (cytochrome c)|g__Escherichia.s__Escherichia_coli\t114.2846087701\n+PWY-3781: aerobic respiration I (cytochrome c)|g__Pseudomonas.s__Pseudomonas_aeruginosa\t74.9156572789\n+PWY-3781: aerobic respiration I (cytochrome c)|unclassified\t36.9962755214\n+PWY-3781: aerobic respiration I (cytochrome c)|g__Helicobacter.s__Helicobacter_pylori\t4.7585206385\n+PWY-3781: aerobic respiration I (cytochrome c)|g__Propionibacterium.s__Propionibacterium_acnes\t3.0760781448\n+PWY-3781: aerobic respiration I (cytochrome c)|g__Deinococcus.s__Deinococcus_radiodurans\t2.4395473535\n+PWY-3781: aerobic respiration I (cytochrome c)|g__Neisseria.s__Neisseria_meningitidis\t1.4220887339\n+PWY66-389: phytol degradation\t979.4805701095\n+PWY66-389: phytol degradation|g__Staphylococcus.s__Staphylococcus_aureus\t310.4884820709\n+PWY66-389: phytol degradation|g__Rhodobacter.s__Rhodobacter_sphaeroides\t295.0258373174\n+PWY66-389: phytol degradation|g__Escherichia.s__Escherichia_coli\t131.9572220185\n+PWY66-389: phytol degradation|g__Pseudomonas.s__Pseudomonas_aeruginosa\t36.1586640369\n+PWY66-389: phytol degradation|g__Acinetobacter.s__Acinetobacter_baumannii\t17.2278325323\n+PWY66-389: phytol degradation|g__Clostridium.s__Clostridium_beijerinckii\t6.7292789582\n+PWY66-389: phytol degradation|g__Propionibacterium.s__Propionibacterium_acnes\t4.2717229621\n+PWY66-389: phytol degradation|g__Deinococcus.s__Deinococcus_radiodurans\t3.1970501558\n+PWY66-389: phytol degradation|unclassified\t1.0145146064\n+PWY-5173: superpathway of acetyl-CoA biosynthesis\t960.5984271439\n+PWY-5173: superpathway of acetyl-CoA biosynthesis|g__Staphylococcus.s__Staphylococcus_epidermidis\t369.2127925716\n+PWY-5173: superpathway of acetyl-CoA biosynthesis|g__Rhodobacter.s__Rhodobacter_sphaeroides\t184.8066347027\n+PWY-5173: superpathway of acetyl-CoA biosynthesis|g__Staphylococcus.s__Staphylococcus_aureus\t155.9950294019\n+PWY-5173: superpathway of acetyl-CoA biosynthesis|g__Streptococcus.s__Streptococcus_mutans\t132.6919877720\n+PWY-5173: superpathway of acetyl-CoA biosynthesis|g__Escherichia.s__Escherichia_coli\t60.4553922962\n+PWY-5173: superpathway of acetyl-CoA biosynthesis|g__Pseudomonas.s__Pseudomonas_aeruginosa\t10.6937687177\n+PWY-5173: superpathway of acetyl-CoA biosynthesis|g__Streptococcus.s__Streptococcus_agalactiae\t4.8481259198\n+PWY-5173: superpathway of acetyl-CoA biosynthesis|g__Acinetobacter.s__Acinetobacter_baumannii\t1.4045480082\n+PWY-5173: superpathway of acetyl-CoA biosynthesis|unclassified\t1.2013427395\n+PWY-5173: superpathway of acetyl-CoA biosynthesis|g__Propionibacterium.s__Propionibacterium_acnes\t1.1988764961\n+PWY-7111: pyruvate fermentation to isobutanol (engineered)\t912.1509918013\n+PWY-7111: pyruvate fermentation to isobutanol (engineered)|g__Staphylococcus.s__Staphylococcus_epidermidis\t254.0802490614\n+PWY-7111: pyruvate fermentation to isobutanol (engineered)|g__Rhodobacter.s__Rhodobacter_sphaeroides\t219.4700532096\n+PWY-7111: pyruvate fermentation to isobutanol (engineered)|g__Staphylococcus.s__Staphylococcus_aureus\t184.0094002055\n+PWY-7111: pyruvate fermentation to isobutanol (engineered)|g__Escherichia.s__Escherichia_coli\t134.5806848081\n+PWY-7111: pyruvate fermentation to isobutanol (engineered)|g__Streptococcus.s__Streptococcus_mutans\t105.3626945686\n+PWY-7111: pyruvate fermentation to isobutanol (engineered)|g__Methanobrevibacter.s__Methanobrevibacter_smithii\t36.6811294465\n+PWY-7111: pyruvate fermentation to isobutanol (engineered)|g__Pseudomonas.s__Pseudomonas_aeruginosa\t16.8691584603\n+PWY-7111: pyruvate fermentation to isobutanol (engineered)|'..b"y of quinolone and alkylquinolone biosynthesis|g__Pseudomonas.s__Pseudomonas_aeruginosa\t8.7871569624\n+PWY-5181: toluene degradation III (aerobic) (via p-cresol)\t9.4768220350\n+PWY-6760: xylose degradation III\t8.0498341681\n+LYSINE-DEG1-PWY: L-lysine degradation XI (mammalian)\t7.8134292537\n+PWY-6672: cis-genanyl-CoA degradation\t6.9084670612\n+PWY-6672: cis-genanyl-CoA degradation|g__Pseudomonas.s__Pseudomonas_aeruginosa\t2.4674381202\n+PWY-6672: cis-genanyl-CoA degradation|g__Acinetobacter.s__Acinetobacter_baumannii\t1.9793128710\n+PWY-6581: spirilloxanthin and 2,2'-diketo-spirilloxanthin biosynthesis\t6.8207617638\n+PWY-6581: spirilloxanthin and 2,2'-diketo-spirilloxanthin biosynthesis|unclassified\t0.9325005511\n+PWY-5183: superpathway of aerobic toluene degradation\t6.2092354547\n+PWY-6383: mono-trans, poly-cis decaprenyl phosphate biosynthesis\t4.8092790379\n+TRIGLSYN-PWY: diacylglycerol and triacylglycerol biosynthesis\t4.5946669738\n+ARGDEG-IV-PWY: L-arginine degradation VIII (arginine oxidase pathway)\t4.1314165669\n+ARGDEG-IV-PWY: L-arginine degradation VIII (arginine oxidase pathway)|unclassified\t0.0472292096\n+PWY-7385: 1,3-propanediol biosynthesis (engineered)\t3.2727699123\n+PWY-6565: superpathway of polyamine biosynthesis III\t3.0724774533\n+PWY-6565: superpathway of polyamine biosynthesis III|unclassified\t0.6506157163\n+PWY-7337: 10-cis-heptadecenoyl-CoA degradation (yeast)\t2.6524638102\n+PWY-7338: 10-trans-heptadecenoyl-CoA degradation (reductase-dependent, yeast)\t2.6524638102\n+PWY-6263: superpathway of menaquinol-8 biosynthesis II\t2.5059205125\n+PWY-6562: norspermidine biosynthesis\t2.1886041799\n+PWY-6562: norspermidine biosynthesis|unclassified\t0.7022305715\n+PWY-5514: UDP-N-acetyl-D-galactosamine biosynthesis II\t2.1199921193\n+PWY-2201: folate transformations I\t2.0735386067\n+PWY-2201: folate transformations I|unclassified\t1.1580586462\n+UDPNACETYLGALSYN-PWY: UDP-N-acetyl-D-glucosamine biosynthesis II\t1.4187052686\n+UDPNACETYLGALSYN-PWY: UDP-N-acetyl-D-glucosamine biosynthesis II|g__Propionibacterium.s__Propionibacterium_acnes\t1.0503113260\n+PWY-7371: 1,4-dihydroxy-6-naphthoate biosynthesis II\t1.2424871748\n+DHGLUCONATE-PYR-CAT-PWY: glucose degradation (oxidative)\t0.9351240467\n+PWY-7373: superpathway of demethylmenaquinol-6 biosynthesis II\t0.7814745906\n+PWY-5420: catechol degradation II (meta-cleavage pathway)\t0.3907944440\n+THREOCAT-PWY: superpathway of L-threonine metabolism\t0.3633843000\n+ILEUDEG-PWY: L-isoleucine degradation I\t0.3384217460\n+ILEUDEG-PWY: L-isoleucine degradation I|unclassified\t0.3102350409\n+PWY-5109: 2-methylbutanoate biosynthesis\t0.3377296788\n+LYSINE-AMINOAD-PWY: L-lysine biosynthesis IV\t0.3065393268\n+PWY-6486: D-galacturonate degradation II\t0.3033074635\n+PWY-6486: D-galacturonate degradation II|unclassified\t0.0612811943\n+PWY-5419: catechol degradation to 2-oxopent-4-enoate II\t0.2239292649\n+PWY-7374: 1,4-dihydroxy-6-naphthoate biosynthesis I\t0.2225632096\n+PWY-5654: 2-amino-3-carboxymuconate semialdehyde degradation to 2-oxopentenoate\t0.2218668573\n+PWY6666-2: dopamine degradation\t0.1687667991\n+PWY6666-2: dopamine degradation|unclassified\t0.1687667991\n+PWY-7413: dTDP-6-deoxy-α-D-allose biosynthesis\t0.1226474527\n+PWY-7413: dTDP-6-deoxy-α-D-allose biosynthesis|unclassified\t0.1188476851\n+PWY-5742: L-arginine degradation IX (arginine:pyruvate transaminase pathway)\t0.1109282575\n+PWY-5742: L-arginine degradation IX (arginine:pyruvate transaminase pathway)|unclassified\t0.0472292096\n+PWY-6117: spermine and spermidine degradation I\t0.1027051153\n+PWY-6117: spermine and spermidine degradation I|unclassified\t0.0997625171\n+PWY-6834: spermidine biosynthesis III\t0.0875565721\n+PWY-6834: spermidine biosynthesis III|unclassified\t0.0845731084\n+PWY-5079: L-phenylalanine degradation III\t0.0714741288\n+PWY-5079: L-phenylalanine degradation III|unclassified\t0.0652061920\n+PWY-7654: (8E,10E)-dodeca-8,10-dienol biosynthesis\t0.0481757443\n+PWY-7654: (8E,10E)-dodeca-8,10-dienol biosynthesis|unclassified\t0.0458917789\n\\ No newline at end of file\n" |
| b |
| diff -r 9959fa526f1a -r c1aca37cb1fc test-data/sample_1_specific_pathways.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample_1_specific_pathways.txt Wed Apr 20 09:15:27 2016 -0400 |
| [ |
| b'@@ -0,0 +1,393 @@\n+id\tname\tabundances\n+GLUCOSE1PMETAB-PWY\tglucose and glucose 1 phosphate degradation|g__Streptococcus.s__Streptococcus_agalactiae\t1410.06644622\n+PWY-621\tsucrose degradation III |g__Streptococcus.s__Streptococcus_agalactiae\t112.79225549\n+PWY-7282\t4 amino 2 methyl 5 phosphomethylpyrimidine biosynthesis |g__Rhodobacter.s__Rhodobacter_sphaeroides\t478.21587188\n+GLUCOSE1PMETAB-PWY\tglucose and glucose 1 phosphate degradation|unclassified\t179.77462326\n+PWY-6731\tstarch degradation III|g__Escherichia.s__Escherichia_coli\t2025.33248781\n+PWY-6897\tthiamin salvage II|g__Staphylococcus.s__Staphylococcus_epidermidis\t6943.50315533\n+PWY-7388\toctanoyl [acyl carrier protein] biosynthesis |g__Pseudomonas.s__Pseudomonas_aeruginosa\t3608.12319483\n+PWY-5860\tsuperpathway of demethylmenaquinol 6 biosynthesis I|g__Escherichia.s__Escherichia_coli\t1639.54069759\n+PWY-1861\tformaldehyde assimilation II |g__Streptococcus.s__Streptococcus_agalactiae\t839.53086925\n+PWY-7208\tsuperpathway of pyrimidine nucleobases salvage|g__Streptococcus.s__Streptococcus_agalactiae\t301.6528534\n+ARGORNPROST-PWY\targinine, ornithine and proline interconversion|unclassified\t119.95840721\n+PWY-7208\tsuperpathway of pyrimidine nucleobases salvage|g__Pseudomonas.s__Pseudomonas_aeruginosa\t2355.29776195\n+PWY-7229\tsuperpathway of adenosine nucleotides de novo biosynthesis I|g__Streptococcus.s__Streptococcus_agalactiae\t361.12670274\n+P4-PWY\tsuperpathway of L lysine, L threonine and L methionine biosynthesis I|g__Pseudomonas.s__Pseudomonas_aeruginosa\t677.11766653\n+PWY-6277\tsuperpathway of 5 aminoimidazole ribonucleotide biosynthesis|g__Streptococcus.s__Streptococcus_agalactiae\t384.06128551\n+GLCMANNANAUT-PWY\tsuperpathway of N acetylglucosamine, N acetylmannosamine and N acetylneuraminate degradation|unclassified\t42.89806203\n+PWY-7234\tinosine 5 phosphate biosynthesis III|g__Staphylococcus.s__Staphylococcus_aureus\t8533.03496704\n+PWY-621\tsucrose degradation III |g__Escherichia.s__Escherichia_coli\t3150.29450022\n+PWY-7413\tdTDP 6 deoxy α D allose biosynthesis\t12.26474527\n+PWY-5345\tsuperpathway of L methionine biosynthesis |g__Escherichia.s__Escherichia_coli\t837.30529432\n+PWY-5154\tL arginine biosynthesis III |g__Pseudomonas.s__Pseudomonas_aeruginosa\t386.2629909\n+PWY-6690\tcinnamate and 3 hydroxycinnamate degradation to 2 oxopent 4 enoate|unclassified\t1.42686388\n+COMPLETE-ARO-PWY\tsuperpathway of aromatic amino acid biosynthesis|g__Rhodobacter.s__Rhodobacter_sphaeroides\t603.00195694\n+HCAMHPDEG-PWY\t3 phenylpropanoate and 3 propanoate degradation to 2 oxopent 4 enoate|g__Escherichia.s__Escherichia_coli\t1403.43643815\n+PWY-6859\tall trans farnesol biosynthesis|g__Streptococcus.s__Streptococcus_agalactiae\t318.54192069\n+PWY66-400\tglycolysis VI |g__Streptococcus.s__Streptococcus_agalactiae\t303.79411134\n+PWY-5973\tcis vaccenate biosynthesis|g__Streptococcus.s__Streptococcus_agalactiae\t447.83907364\n+PWY-6672\tcis genanyl CoA degradation|g__Pseudomonas.s__Pseudomonas_aeruginosa\t246.74381202\n+P105-PWY\tTCA cycle IV |g__Pseudomonas.s__Pseudomonas_aeruginosa\t346.96109281\n+PWY-4702\tphytate degradation I|unclassified\t88.68668132\n+PWY-7242\tD fructuronate degradation|g__Streptococcus.s__Streptococcus_agalactiae\t202.56826561\n+PWY-6609\tadenine and adenosine salvage III|g__Pseudomonas.s__Pseudomonas_aeruginosa\t492.9281104\n+PWY-6124\tinosine 5 phosphate biosynthesis II|g__Methanobrevibacter.s__Methanobrevibacter_smithii\t3405.18193479\n+PWY-6562\tnorspermidine biosynthesis|unclassified\t70.22305715\n+NAGLIPASYN-PWY\tlipid IVA biosynthesis|unclassified\t25.03978499\n+PWY0-1277\t3 phenylpropanoate and 3 propanoate degradation|g__Escherichia.s__Escherichia_coli\t2473.1533402\n+GLYCOL-GLYOXDEG-PWY\tsuperpathway of glycol metabolism and degradation|g__Pseudomonas.s__Pseudomonas_aeruginosa\t675.72913268\n+PWY-6969\tTCA cycle V (2 oxoglutarate\t7590.86231693\n+PWY-5686\tUMP biosynthesis|g__Methanobrevibacter.s__Methanobrevibacter_smithii\t2597.42400205\n+PWY-7294\txylose degradation IV\t3457.02196873\n+PWY-7187\tpyrimidine deoxyribonucleot'..b' ornithine degradation|unclassified\t67.59290738\n+PWY-6168\tflavin biosynthesis III |g__Escherichia.s__Escherichia_coli\t1076.61192214\n+PWY-7228\tsuperpathway of guanosine nucleotides de novo biosynthesis I|g__Streptococcus.s__Streptococcus_agalactiae\t339.2748428\n+PWY-6123\tinosine 5 phosphate biosynthesis I|g__Staphylococcus.s__Staphylococcus_aureus\t8629.38522048\n+PWY-7664\toleate biosynthesis IV |g__Pseudomonas.s__Pseudomonas_aeruginosa\t2728.84413265\n+DAPLYSINESYN-PWY\tL lysine biosynthesis I|g__Pseudomonas.s__Pseudomonas_aeruginosa\t780.13280579\n+ALLANTOINDEG-PWY\tsuperpathway of allantoin degradation in yeast|unclassified\t184.58699889\n+P125-PWY\tsuperpathway of butanediol biosynthesis|unclassified\t50.56326117\n+PWY-7118\tchitin degradation to ethanol|unclassified\t179.48569416\n+PWY-6167\tflavin biosynthesis II \t4728.07707794\n+PWY-841\tsuperpathway of purine nucleotides de novo biosynthesis I|g__Staphylococcus.s__Staphylococcus_aureus\t11184.2607862\n+HCAMHPDEG-PWY\t3 phenylpropanoate and 3 propanoate degradation to 2 oxopent 4 enoate|unclassified\t1.42686388\n+PWY-5850\tsuperpathway of menaquinol 6 biosynthesis I|g__Escherichia.s__Escherichia_coli\t2086.15005453\n+PWY-7409\tphospholipid remodeling \t2857.98178304\n+FOLSYN-PWY\tsuperpathway of tetrahydrofolate biosynthesis and salvage|g__Pseudomonas.s__Pseudomonas_aeruginosa\t415.68053269\n+PWY-6969\tTCA cycle V (2 oxoglutarate\t346.96109281\n+SALVADEHYPOX-PWY\tadenosine nucleotides degradation II|g__Staphylococcus.s__Staphylococcus_aureus\t796.46617638\n+PWY66-409\tsuperpathway of purine nucleotide salvage|g__Escherichia.s__Escherichia_coli\t1182.85263435\n+PWY-6147\t6 hydroxymethyl dihydropterin diphosphate biosynthesis I|g__Rhodobacter.s__Rhodobacter_sphaeroides\t600.76339368\n+URSIN-PWY\tureide biosynthesis|g__Pseudomonas.s__Pseudomonas_aeruginosa\t346.33151921\n+PENTOSE-P-PWY\tpentose phosphate pathway|g__Pseudomonas.s__Pseudomonas_aeruginosa\t232.40561581\n+PWY0-1061\tsuperpathway of L alanine biosynthesis|g__Streptococcus.s__Streptococcus_agalactiae\t629.81986142\n+PWY-7234\tinosine 5 phosphate biosynthesis III|g__Streptococcus.s__Streptococcus_agalactiae\t388.54431864\n+ARGDEG-PWY\tsuperpathway of L arginine, putrescine, and 4 aminobutanoate degradation|g__Pseudomonas.s__Pseudomonas_aeruginosa\t792.37856895\n+PWY4FS-8\tphosphatidylglycerol biosynthesis II |g__Pseudomonas.s__Pseudomonas_aeruginosa\t366.47566208\n+OANTIGEN-PWY\tO antigen building blocks biosynthesis |g__Methanobrevibacter.s__Methanobrevibacter_smithii\t3062.91191006\n+3-HYDROXYPHENYLACETATE-DEGRADATION-PWY\t4 hydroxyphenylacetate degradation|g__Escherichia.s__Escherichia_coli\t1868.56730475\n+ARO-PWY\tchorismate biosynthesis I|g__Rhodobacter.s__Rhodobacter_sphaeroides\t531.17556088\n+PWY-5079\tL phenylalanine degradation III\t7.14741288\n+PWY-6305\tputrescine biosynthesis IV|g__Methanobrevibacter.s__Methanobrevibacter_smithii\t1780.01452698\n+CATECHOL-ORTHO-CLEAVAGE-PWY\tcatechol degradation to β ketoadipate|g__Rhodobacter.s__Rhodobacter_sphaeroides\t480.71275029\n+PWY-7184\tpyrimidine deoxyribonucleotides de novo biosynthesis I|g__Staphylococcus.s__Staphylococcus_aureus\t11346.2826023\n+PWY-5857\tubiquinol 10 biosynthesis |g__Pseudomonas.s__Pseudomonas_aeruginosa\t1649.4470132\n+PWY-4702\tphytate degradation I|g__Staphylococcus.s__Staphylococcus_aureus\t666.66666667\n+PWY-6703\tpreQ0 biosynthesis|g__Pseudomonas.s__Pseudomonas_aeruginosa\t796.05490757\n+PWY-6507\t4 deoxy L threo hex 4 enopyranuronate degradation|g__Streptococcus.s__Streptococcus_agalactiae\t223.47351181\n+PWY-6435\t4 hydroxybenzoate biosynthesis V|g__Staphylococcus.s__Staphylococcus_aureus\t9409.37733628\n+PWY-7199\tpyrimidine deoxyribonucleosides salvage|g__Staphylococcus.s__Staphylococcus_aureus\t10064.1302003\n+CALVIN-PWY\tCalvin Benson Bassham cycle|g__Streptococcus.s__Streptococcus_agalactiae\t616.19648266\n+PWY-5855\tubiquinol 7 biosynthesis |g__Pseudomonas.s__Pseudomonas_aeruginosa\t1649.4470132\n+PWY0-845\tsuperpathway of pyridoxal 5 phosphate biosynthesis and salvage|g__Rhodobacter.s__Rhodobacter_sphaeroides\t779.91889375\n' |
| b |
| diff -r 9959fa526f1a -r c1aca37cb1fc test-data/sample_2_pathway_abundances.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample_2_pathway_abundances.tabular Wed Apr 20 09:15:27 2016 -0400 |
| b |
| b'@@ -0,0 +1,3256 @@\n+# Pathway\thumann2_Abundance\n+PWY-3781: aerobic respiration I (cytochrome c)\t1379.3117561632\n+PWY-3781: aerobic respiration I (cytochrome c)|g__Deinococcus.s__Deinococcus_radiodurans\t519.6406813052\n+PWY-3781: aerobic respiration I (cytochrome c)|g__Propionibacterium.s__Propionibacterium_acnes\t144.1604040177\n+PWY-3781: aerobic respiration I (cytochrome c)|g__Acinetobacter.s__Acinetobacter_baumannii\t106.6125425404\n+PWY-3781: aerobic respiration I (cytochrome c)|g__Staphylococcus.s__Staphylococcus_epidermidis\t85.2211671136\n+PWY-3781: aerobic respiration I (cytochrome c)|g__Helicobacter.s__Helicobacter_pylori\t74.8651278743\n+PWY-3781: aerobic respiration I (cytochrome c)|g__Rhodobacter.s__Rhodobacter_sphaeroides\t73.5687095282\n+PWY-3781: aerobic respiration I (cytochrome c)|g__Neisseria.s__Neisseria_meningitidis\t68.4543838944\n+PWY-3781: aerobic respiration I (cytochrome c)|g__Escherichia.s__Escherichia_coli\t35.0459201375\n+PWY-3781: aerobic respiration I (cytochrome c)|g__Actinomyces.s__Actinomyces_odontolyticus\t27.7258262062\n+PWY-3781: aerobic respiration I (cytochrome c)|g__Bacteroides.s__Bacteroides_vulgatus\t23.7293286574\n+PWY-3781: aerobic respiration I (cytochrome c)|g__Pseudomonas.s__Pseudomonas_aeruginosa\t23.1768361723\n+PWY-3781: aerobic respiration I (cytochrome c)|g__Staphylococcus.s__Staphylococcus_aureus\t21.0846546528\n+PWY-3781: aerobic respiration I (cytochrome c)|g__Listeria.s__Listeria_monocytogenes\t19.6307167087\n+PWY-3781: aerobic respiration I (cytochrome c)|unclassified\t11.1898637960\n+PWY-3781: aerobic respiration I (cytochrome c)|g__Bacillus.s__Bacillus_cereus_thuringiensis\t7.4084156305\n+PWY66-389: phytol degradation\t1267.9982204952\n+PWY66-389: phytol degradation|g__Deinococcus.s__Deinococcus_radiodurans\t409.6569509177\n+PWY66-389: phytol degradation|g__Acinetobacter.s__Acinetobacter_baumannii\t297.6438567470\n+PWY66-389: phytol degradation|g__Propionibacterium.s__Propionibacterium_acnes\t48.3073518595\n+PWY66-389: phytol degradation|g__Staphylococcus.s__Staphylococcus_aureus\t37.4372936189\n+PWY66-389: phytol degradation|g__Bacteroides.s__Bacteroides_vulgatus\t35.8965739105\n+PWY66-389: phytol degradation|g__Rhodobacter.s__Rhodobacter_sphaeroides\t34.8552095886\n+PWY66-389: phytol degradation|g__Neisseria.s__Neisseria_meningitidis\t19.1990040023\n+PWY66-389: phytol degradation|g__Escherichia.s__Escherichia_coli\t18.6739557286\n+PWY66-389: phytol degradation|g__Clostridium.s__Clostridium_beijerinckii\t18.4307070366\n+PWY66-389: phytol degradation|g__Pseudomonas.s__Pseudomonas_aeruginosa\t13.3350808028\n+PWY66-389: phytol degradation|g__Bacillus.s__Bacillus_cereus_thuringiensis\t8.9117743198\n+PWY66-389: phytol degradation|g__Listeria.s__Listeria_monocytogenes\t8.5387077686\n+PWY66-389: phytol degradation|g__Enterococcus.s__Enterococcus_faecalis\t6.3776203668\n+PWY66-389: phytol degradation|unclassified\t4.1191815981\n+FAO-PWY: fatty acid β-oxidation I\t1145.6793386604\n+FAO-PWY: fatty acid β-oxidation I|g__Deinococcus.s__Deinococcus_radiodurans\t576.2091248906\n+FAO-PWY: fatty acid β-oxidation I|g__Acinetobacter.s__Acinetobacter_baumannii\t186.8198587635\n+FAO-PWY: fatty acid β-oxidation I|g__Rhodobacter.s__Rhodobacter_sphaeroides\t20.1692630116\n+FAO-PWY: fatty acid β-oxidation I|g__Clostridium.s__Clostridium_beijerinckii\t19.4488549916\n+FAO-PWY: fatty acid β-oxidation I|g__Staphylococcus.s__Staphylococcus_aureus\t18.1117843293\n+FAO-PWY: fatty acid β-oxidation I|g__Escherichia.s__Escherichia_coli\t14.3558600015\n+FAO-PWY: fatty acid β-oxidation I|g__Pseudomonas.s__Pseudomonas_aeruginosa\t9.8141140410\n+FAO-PWY: fatty acid β-oxidation I|unclassified\t7.3784150576\n+FAO-PWY: fatty acid β-oxidation I|g__Bacillus.s__Bacillus_cereus_thuringiensis\t3.1567137570\n+PWY-5136: fatty acid β-oxidation II (peroxisome)\t1113.5630510005\n+PWY-5136: fatty acid β-oxidation II (peroxisome)|g__Deinococcus.s__Deinococcus_radiodurans\t446.1957128338\n+PWY-5136: fatty acid β-oxidation II (peroxisome)|'..b"bacter.s__Methanobrevibacter_smithii\t2.1380081900\n+PWY6666-2: dopamine degradation\t4.4149880080\n+PWY6666-2: dopamine degradation|g__Bacillus.s__Bacillus_cereus_thuringiensis\t4.4149880080\n+PWY-6863: pyruvate fermentation to hexanol\t4.3553809296\n+PWY-6165: chorismate biosynthesis II (archaea)\t4.2990575319\n+KDO-NAGLIPASYN-PWY: superpathway of (Kdo)2-lipid A biosynthesis\t4.2818581142\n+KDO-NAGLIPASYN-PWY: superpathway of (Kdo)2-lipid A biosynthesis|g__Escherichia.s__Escherichia_coli\t3.6340902033\n+PWY-7374: 1,4-dihydroxy-6-naphthoate biosynthesis I\t4.2617944030\n+PWY-7374: 1,4-dihydroxy-6-naphthoate biosynthesis I|g__Deinococcus.s__Deinococcus_radiodurans\t4.2564087175\n+PWY-7332: superpathway of UDP-N-acetylglucosamine-derived O-antigen building blocks biosynthesis\t4.2113090113\n+DHGLUCONATE-PYR-CAT-PWY: glucose degradation (oxidative)\t4.0519573172\n+DHGLUCONATE-PYR-CAT-PWY: glucose degradation (oxidative)|g__Pseudomonas.s__Pseudomonas_aeruginosa\t2.4338139554\n+PWY-4722: creatinine degradation II\t3.5859562242\n+PWY0-1533: methylphosphonate degradation I\t3.5513449231\n+PWY0-1533: methylphosphonate degradation I|g__Escherichia.s__Escherichia_coli\t3.5433547083\n+PWY-6581: spirilloxanthin and 2,2'-diketo-spirilloxanthin biosynthesis\t3.3705679473\n+PWY-6467: Kdo transfer to lipid IVA III (Chlamydia)\t3.3228938386\n+PWY-6467: Kdo transfer to lipid IVA III (Chlamydia)|g__Escherichia.s__Escherichia_coli\t3.3228938386\n+HCAMHPDEG-PWY: 3-phenylpropanoate and 3-(3-hydroxyphenyl)propanoate degradation to 2-oxopent-4-enoate\t3.0173944072\n+PWY-6690: cinnamate and 3-hydroxycinnamate degradation to 2-oxopent-4-enoate\t3.0173944072\n+PWY-5419: catechol degradation to 2-oxopent-4-enoate II\t2.9169750560\n+PWY-5419: catechol degradation to 2-oxopent-4-enoate II|unclassified\t0.5038002752\n+LYSINE-DEG1-PWY: L-lysine degradation XI (mammalian)\t2.8294061510\n+PWY66-388: fatty acid α-oxidation III\t2.7616868171\n+PWY66-388: fatty acid α-oxidation III|g__Pseudomonas.s__Pseudomonas_aeruginosa\t2.5883879283\n+PWY-7286: 7-(3-amino-3-carboxypropyl)-wyosine biosynthesis\t2.3998964359\n+PWY-6660: 2-heptyl-3-hydroxy-4(1H)-quinolone biosynthesis\t1.6605058007\n+PWY-6660: 2-heptyl-3-hydroxy-4(1H)-quinolone biosynthesis|g__Pseudomonas.s__Pseudomonas_aeruginosa\t1.3889133405\n+PWY-6662: superpathway of quinolone and alkylquinolone biosynthesis\t1.4885805495\n+PWY-6662: superpathway of quinolone and alkylquinolone biosynthesis|g__Pseudomonas.s__Pseudomonas_aeruginosa\t1.3055003111\n+PWY-5430: meta cleavage pathway of aromatic compounds\t1.2629316846\n+PWY-5430: meta cleavage pathway of aromatic compounds|unclassified\t0.1894157642\n+PWY-7185: UTP and CTP dephosphorylation I\t0.9519614057\n+PWY-7185: UTP and CTP dephosphorylation I|unclassified\t0.8686345617\n+PWY-6486: D-galacturonate degradation II\t0.8896462620\n+PWY-622: starch biosynthesis\t0.7684320984\n+PWY-5654: 2-amino-3-carboxymuconate semialdehyde degradation to 2-oxopentenoate\t0.7364822065\n+PWY-7312: dTDP-D-β-fucofuranose biosynthesis\t0.5880445130\n+PWY-7312: dTDP-D-β-fucofuranose biosynthesis|unclassified\t0.4918491014\n+PWY-5872: ubiquinol-10 biosynthesis (eukaryotic)\t0.4719209027\n+PWY-5532: adenosine nucleotides degradation IV\t0.3384452492\n+LYSINE-AMINOAD-PWY: L-lysine biosynthesis IV\t0.3342290902\n+LYSINE-AMINOAD-PWY: L-lysine biosynthesis IV|unclassified\t0.2498537656\n+PWY-6518: glycocholate metabolism (bacteria)\t0.3102285654\n+PWY-7046: 4-coumarate degradation (anaerobic)\t0.2023459486\n+PWY-7046: 4-coumarate degradation (anaerobic)|unclassified\t0.1945543615\n+PWY-5534: propylene degradation\t0.1654024753\n+PWY-6834: spermidine biosynthesis III\t0.1311856104\n+PWY-6834: spermidine biosynthesis III|unclassified\t0.1285090982\n+PWY-6432: curcuminoid biosynthesis\t0.0768372594\n+PWY-6432: curcuminoid biosynthesis|unclassified\t0.0640501503\n+PWY-3481: superpathway of L-phenylalanine and L-tyrosine biosynthesis\t0.0659290655\n+PWY-3481: superpathway of L-phenylalanine and L-tyrosine biosynthesis|unclassified\t0.0617837999\n\\ No newline at end of file\n" |
| b |
| diff -r 9959fa526f1a -r c1aca37cb1fc test-data/sample_2_specific_pathways.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample_2_specific_pathways.txt Wed Apr 20 09:15:27 2016 -0400 |
| [ |
| b'@@ -0,0 +1,1336 @@\n+id\tname\tabundances\n+PWY-6123\tinosine 5 phosphate biosynthesis I|g__Streptococcus.s__Streptococcus_mitis_oralis_pneumoniae\t3694.54369841\n+PWY-7111\tpyruvate fermentation to isobutanol |g__Streptococcus.s__Streptococcus_mitis_oralis_pneumoniae\t7136.11057394\n+PWY-7187\tpyrimidine deoxyribonucleotides de novo biosynthesis II|g__Bacteroides.s__Bacteroides_vulgatus\t1482.08811185\n+PWY-5392\treductive TCA cycle II|unclassified\t13.94276095\n+PWY-6126\tsuperpathway of adenosine nucleotides de novo biosynthesis II|g__Neisseria.s__Neisseria_meningitidis\t1351.86626275\n+PWY-5855\tubiquinol 7 biosynthesis |g__Acinetobacter.s__Acinetobacter_baumannii\t3461.49933469\n+PWY0-1061\tsuperpathway of L alanine biosynthesis|g__Streptococcus.s__Streptococcus_mitis_oralis_pneumoniae\t2801.26577532\n+ARGORNPROST-PWY\targinine, ornithine and proline interconversion|g__Enterococcus.s__Enterococcus_faecalis\t229.86451776\n+PWY-841\tsuperpathway of purine nucleotides de novo biosynthesis I|g__Streptococcus.s__Streptococcus_mitis_oralis_pneumoniae\t3239.55702033\n+PWY-6125\tsuperpathway of guanosine nucleotides de novo biosynthesis II|g__Neisseria.s__Neisseria_meningitidis\t1264.65018972\n+PWY-5918\tsuperpathay of heme biosynthesis from glutamate|g__Acinetobacter.s__Acinetobacter_baumannii\t3739.74164481\n+PWY-5189\ttetrapyrrole biosynthesis II |g__Deinococcus.s__Deinococcus_radiodurans\t939.65853472\n+PWY-1042\tglycolysis IV |g__Propionibacterium.s__Propionibacterium_acnes\t4307.94946602\n+HISDEG-PWY\tL histidine degradation I|g__Propionibacterium.s__Propionibacterium_acnes\t3254.94984635\n+PWY-5173\tsuperpathway of acetyl CoA biosynthesis|g__Streptococcus.s__Streptococcus_mitis_oralis_pneumoniae\t2519.87744949\n+FOLSYN-PWY\tsuperpathway of tetrahydrofolate biosynthesis and salvage|g__Propionibacterium.s__Propionibacterium_acnes\t1675.37062714\n+PWY-6895\tsuperpathway of thiamin diphosphate biosynthesis II|unclassified\t64.56529023\n+PWY-7388\toctanoyl [acyl carrier protein] biosynthesis |g__Streptococcus.s__Streptococcus_mitis_oralis_pneumoniae\t1522.60994915\n+PEPTIDOGLYCANSYN-PWY\tpeptidoglycan biosynthesis I |g__Bacteroides.s__Bacteroides_vulgatus\t2160.13104462\n+PWY-4984\turea cycle|g__Bacteroides.s__Bacteroides_vulgatus\t2013.67758619\n+3-HYDROXYPHENYLACETATE-DEGRADATION-PWY\t4 hydroxyphenylacetate degradation|g__Deinococcus.s__Deinococcus_radiodurans\t11558.1286712\n+PWY-5695\turate biosynthesis inosine 5 phosphate degradation|g__Enterococcus.s__Enterococcus_faecalis\t256.90178056\n+BRANCHED-CHAIN-AA-SYN-PWY\tsuperpathway of branched amino acid biosynthesis|g__Streptococcus.s__Streptococcus_mitis_oralis_pneumoniae\t3873.13594163\n+PEPTIDOGLYCANSYN-PWY\tpeptidoglycan biosynthesis I |g__Listeria.s__Listeria_monocytogenes\t724.9534439\n+SER-GLYSYN-PWY\tsuperpathway of L serine and glycine biosynthesis I|g__Bacteroides.s__Bacteroides_vulgatus\t2896.52791818\n+PWY-7219\tadenosine ribonucleotides de novo biosynthesis|g__Streptococcus.s__Streptococcus_mitis_oralis_pneumoniae\t3526.58041039\n+PWY-6151\tS adenosyl L methionine cycle I|g__Acinetobacter.s__Acinetobacter_baumannii\t3884.95626038\n+COA-PWY\tcoenzyme A biosynthesis I|g__Streptococcus.s__Streptococcus_mitis_oralis_pneumoniae\t2145.77462112\n+PWY-6387\tUDP N acetylmuramoyl pentapeptide biosynthesis I |g__Enterococcus.s__Enterococcus_faecalis\t413.84697579\n+PWY0-162\tsuperpathway of pyrimidine ribonucleotides de novo biosynthesis|g__Bacteroides.s__Bacteroides_vulgatus\t2788.62370201\n+PWY0-1296\tpurine ribonucleosides degradation|g__Listeria.s__Listeria_monocytogenes\t1662.84626817\n+PWY0-162\tsuperpathway of pyrimidine ribonucleotides de novo biosynthesis|g__Helicobacter.s__Helicobacter_pylori\t2256.50698827\n+PWY-6386\tUDP N acetylmuramoyl pentapeptide biosynthesis II |g__Acinetobacter.s__Acinetobacter_baumannii\t5271.876702\n+PWY-6317\tgalactose degradation I |g__Listeria.s__Listeria_monocytogenes\t918.92772969\n+PWY-5910\tsuperpathway of geranylgeranyldiphosphate biosynthesis I |g__Enterococcus.s__Enterococcus_faecalis\t406.73179148\n+PWY-6168\tflavin biosynthesis III'..b'esis I|g__Neisseria.s__Neisseria_meningitidis\t1703.07371128\n+PWY-7229\tsuperpathway of adenosine nucleotides de novo biosynthesis I|g__Actinomyces.s__Actinomyces_odontolyticus\t1047.3630038\n+PWY-7221\tguanosine ribonucleotides de novo biosynthesis|g__Listeria.s__Listeria_monocytogenes\t602.0224203\n+PWY-7184\tpyrimidine deoxyribonucleotides de novo biosynthesis I|g__Neisseria.s__Neisseria_meningitidis\t1063.82344404\n+PWY-7220\tadenosine deoxyribonucleotides de novo biosynthesis II|g__Listeria.s__Listeria_monocytogenes\t943.08991771\n+PWYG-321\tmycolate biosynthesis|g__Listeria.s__Listeria_monocytogenes\t727.33694636\n+PWY-6588\tpyruvate fermentation to acetone|g__Helicobacter.s__Helicobacter_pylori\t1842.02586387\n+PWY-6628\tsuperpathway of L phenylalanine biosynthesis|g__Neisseria.s__Neisseria_meningitidis\t2325.31672002\n+ARGSYNBSUB-PWY\tL arginine biosynthesis II |g__Acinetobacter.s__Acinetobacter_baumannii\t5640.53034458\n+HSERMETANA-PWY\tL methionine biosynthesis III|g__Bacteroides.s__Bacteroides_vulgatus\t3812.82018369\n+PWY-7539\t6 hydroxymethyl dihydropterin diphosphate biosynthesis III |g__Neisseria.s__Neisseria_meningitidis\t1016.73003305\n+PWY-7198\tpyrimidine deoxyribonucleotides de novo biosynthesis IV|g__Propionibacterium.s__Propionibacterium_acnes\t3089.26224286\n+PWY-7539\t6 hydroxymethyl dihydropterin diphosphate biosynthesis III |g__Propionibacterium.s__Propionibacterium_acnes\t640.34891279\n+PWY-5872\tubiquinol 10 biosynthesis \t47.19209027\n+PWY-6936\tseleno amino acid biosynthesis|g__Enterococcus.s__Enterococcus_faecalis\t575.37669038\n+PWY-5910\tsuperpathway of geranylgeranyldiphosphate biosynthesis I |g__Listeria.s__Listeria_monocytogenes\t465.60089664\n+PWY-7222\tguanosine deoxyribonucleotides de novo biosynthesis II|g__Streptococcus.s__Streptococcus_mitis_oralis_pneumoniae\t4569.16166358\n+PWY66-400\tglycolysis VI |g__Listeria.s__Listeria_monocytogenes\t824.96499562\n+FASYN-ELONG-PWY\tfatty acid elongation saturated|g__Enterococcus.s__Enterococcus_faecalis\t1735.8151961\n+PWY-3781\taerobic respiration I |g__Bacteroides.s__Bacteroides_vulgatus\t2372.93286574\n+PWY-6126\tsuperpathway of adenosine nucleotides de novo biosynthesis II|g__Helicobacter.s__Helicobacter_pylori\t3229.2140178\n+PWY-6703\tpreQ0 biosynthesis|g__Clostridium.s__Clostridium_beijerinckii\t456.48187263\n+PWY-6121\t5 aminoimidazole ribonucleotide biosynthesis I|g__Actinomyces.s__Actinomyces_odontolyticus\t656.48352888\n+DAPLYSINESYN-PWY\tL lysine biosynthesis I|g__Neisseria.s__Neisseria_meningitidis\t1713.17916266\n+PWY-5100\tpyruvate fermentation to acetate and lactate II|g__Actinomyces.s__Actinomyces_odontolyticus\t711.05039042\n+PWY-5659\tGDP mannose biosynthesis|g__Bacteroides.s__Bacteroides_vulgatus\t5067.97426256\n+PWY-7373\tsuperpathway of demethylmenaquinol 6 biosynthesis II|g__Helicobacter.s__Helicobacter_pylori\t1006.81238724\n+PWY-7663\tgondoate biosynthesis |g__Neisseria.s__Neisseria_meningitidis\t4680.40950351\n+ARO-PWY\tchorismate biosynthesis I|g__Acinetobacter.s__Acinetobacter_baumannii\t5469.17722481\n+PWY-841\tsuperpathway of purine nucleotides de novo biosynthesis I|g__Acinetobacter.s__Acinetobacter_baumannii\t3027.23954619\n+P108-PWY\tpyruvate fermentation to propanoate I|unclassified\t80.78380624\n+UDPNAGSYN-PWY\tUDP N acetyl D glucosamine biosynthesis I|g__Bacillus.s__Bacillus_cereus_thuringiensis\t271.55477416\n+PWY-6891\tthiazole biosynthesis II |g__Bacillus.s__Bacillus_cereus_thuringiensis\t290.80786445\n+PWY-4041\tγ glutamyl cycle|g__Enterococcus.s__Enterococcus_faecalis\t813.17944374\n+PWY-6163\tchorismate biosynthesis from 3 dehydroquinate|g__Listeria.s__Listeria_monocytogenes\t913.1636705\n+PWY66-389\tphytol degradation|g__Listeria.s__Listeria_monocytogenes\t853.87077686\n+OANTIGEN-PWY\tO antigen building blocks biosynthesis |g__Clostridium.s__Clostridium_beijerinckii\t485.31186564\n+PWY-7392\ttaxadiene biosynthesis |g__Propionibacterium.s__Propionibacterium_acnes\t2628.10374094\n+PWY-6125\tsuperpathway of guanosine nucleotides de novo biosynthesis II|g__Deinococcus.s__Deinococcus_radiodurans\t18402.8474421\n' |
| b |
| diff -r 9959fa526f1a -r c1aca37cb1fc test-data/sample_comparison_log.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample_comparison_log.txt Wed Apr 20 09:15:27 2016 -0400 |
| b |
| @@ -0,0 +1,12 @@ +Similar between all samples: 1920 +Specific to samples: + sample1 + All: 2312 + Number of specific characteristics: 392 + Percentage of specific characteristics: 16.955017301 + Relative abundance of specific characteristics(%): 643695.745806 + sample2 + All: 3255 + Number of specific characteristics: 1335 + Percentage of specific characteristics: 41.0138248848 + Relative abundance of specific characteristics(%): 3723960.40921 |
| b |
| diff -r 9959fa526f1a -r c1aca37cb1fc test-data/sample_similar_pathways.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample_similar_pathways.tabular Wed Apr 20 09:15:27 2016 -0400 |
| [ |
| b'@@ -0,0 +1,1921 @@\n+id\tname\tsample1\tsample2\n+PWY-6527\tstachyose degradation|g__Streptococcus.s__Streptococcus_mutans\t9089.59894354\t1696.97295223\n+PWY-6471\tpeptidoglycan biosynthesis IV \t46455.865627\t30449.8634207\n+PWY-7208\tsuperpathway of pyrimidine nucleobases salvage|g__Rhodobacter.s__Rhodobacter_sphaeroides\t12559.4677571\t1282.55432956\n+PWY-7288\tfatty acid β oxidation \t12818.3639901\t25828.6507825\n+PWY-3841\tfolate transformations II|g__Escherichia.s__Escherichia_coli\t3007.20583149\t217.72486044\n+PWY-6737\tstarch degradation V|unclassified\t48.21577448\t239.03206251\n+PWY0-1297\tsuperpathway of purine deoxyribonucleosides degradation|g__Staphylococcus.s__Staphylococcus_epidermidis\t9039.67328714\t1589.30574604\n+PWY-5659\tGDP mannose biosynthesis|g__Acinetobacter.s__Acinetobacter_baumannii\t172.93621006\t4543.25980432\n+PWY-2942\tL lysine biosynthesis III|g__Streptococcus.s__Streptococcus_mutans\t4710.2025552\t708.88601201\n+PWY-6151\tS adenosyl L methionine cycle I\t45554.1733597\t42591.852733\n+SALVADEHYPOX-PWY\tadenosine nucleotides degradation II\t88803.4244676\t102915.149017\n+PWY-6596\tadenosine nucleotides degradation I\t7817.66872493\t696.2294504\n+PWY4LZ-257\tsuperpathway of fermentation \t44732.9715391\t35196.3430939\n+ILEUDEG-PWY\tL isoleucine degradation I\t33.8421746\t6967.21446351\n+PWY0-1261\tanhydromuropeptides recycling|g__Escherichia.s__Escherichia_coli\t5164.50768682\t671.73572925\n+PANTOSYN-PWY\tpantothenate and coenzyme A biosynthesis I|g__Staphylococcus.s__Staphylococcus_epidermidis\t10239.9838748\t583.91715667\n+PWY-5686\tUMP biosynthesis|g__Streptococcus.s__Streptococcus_mutans\t6754.11537711\t798.00767542\n+PWY-5384\tsucrose degradation IV \t12240.4968895\t9746.7324837\n+PWY-6277\tsuperpathway of 5 aminoimidazole ribonucleotide biosynthesis|g__Staphylococcus.s__Staphylococcus_aureus\t13369.9763528\t1138.58445146\n+PWY-7357\tthiamin formation from pyrithiamine and oxythiamine |g__Staphylococcus.s__Staphylococcus_epidermidis\t7605.96092233\t1506.9159832\n+PWY-5676\tacetyl CoA fermentation to butanoate II|g__Clostridium.s__Clostridium_beijerinckii\t834.72187681\t2820.816865\n+GLUTORN-PWY\tL ornithine biosynthesis|g__Rhodobacter.s__Rhodobacter_sphaeroides\t2679.42319429\t806.11037888\n+PWY-5676\tacetyl CoA fermentation to butanoate II|unclassified\t293.27344931\t313.4611172\n+PWY-6107\tchlorosalicylate degradation\t4990.49166626\t3707.99522741\n+PWY-5514\tUDP N acetyl D galactosamine biosynthesis II\t211.99921193\t8344.45133876\n+HEMESYN2-PWY\theme biosynthesis II |g__Rhodobacter.s__Rhodobacter_sphaeroides\t13472.0925007\t1713.65799734\n+SER-GLYSYN-PWY\tsuperpathway of L serine and glycine biosynthesis I|g__Acinetobacter.s__Acinetobacter_baumannii\t165.52210569\t5261.09986526\n+PWY-6467\tKdo transfer to lipid IVA III \t1326.69762557\t332.28938386\n+PWY-5971\tpalmitate biosynthesis II |unclassified\t328.78037799\t707.87369542\n+PWY-6313\tserotonin degradation|g__Propionibacterium.s__Propionibacterium_acnes\t257.91056362\t3253.85903121\n+PWY-5897\tsuperpathway of menaquinol 11 biosynthesis\t21209.4938493\t15529.8979214\n+PWY-2942\tL lysine biosynthesis III|g__Clostridium.s__Clostridium_beijerinckii\t372.91948736\t1644.65015852\n+PWY-6305\tputrescine biosynthesis IV|g__Rhodobacter.s__Rhodobacter_sphaeroides\t2264.19577283\t409.21191468\n+HEMESYN2-PWY\theme biosynthesis II |g__Neisseria.s__Neisseria_meningitidis\t160.47842097\t2460.45875987\n+PWY-6305\tputrescine biosynthesis IV\t19202.9873681\t14135.5882465\n+PWY-7219\tadenosine ribonucleotides de novo biosynthesis|unclassified\t316.23278205\t406.96069748\n+HEME-BIOSYNTHESIS-II\theme biosynthesis I |g__Rhodobacter.s__Rhodobacter_sphaeroides\t13109.3800959\t1763.21900128\n+ANAEROFRUCAT-PWY\thomolactic fermentation|g__Clostridium.s__Clostridium_beijerinckii\t604.47752551\t1298.26997095\n+PWY-6307\tL tryptophan degradation X |g__Propionibacterium.s__Propionibacterium_acnes\t209.13755224\t2687.36440723\n+PWY-6606\tguanosine nucleotides degradation II|g__Rhodobacter.s__Rhodobacter_sphaeroides\t2736.23201469\t471.84886441\n+PWY-5189\ttetrapyrrole biosynthesis II |g__Staphylococcus.s__Staphylococcus'..b'_baumannii\t311.86743823\t5092.62189788\n+PWY-7198\tpyrimidine deoxyribonucleotides de novo biosynthesis IV|unclassified\t497.58534601\t921.96101244\n+PWY0-1479\ttRNA processing|unclassified\t53.90015148\t65.20708513\n+PWY-5103\tL isoleucine biosynthesis III|g__Staphylococcus.s__Staphylococcus_aureus\t12414.2746766\t1786.69711145\n+PWY-4041\tγ glutamyl cycle\t30349.4757439\t14586.7772214\n+COLANSYN-PWY\tcolanic acid building blocks biosynthesis|unclassified\t16.96524789\t206.11126006\n+PWY-7357\tthiamin formation from pyrithiamine and oxythiamine |g__Clostridium.s__Clostridium_beijerinckii\t367.13964071\t1248.77414621\n+PWY-5791\t1,4 dihydroxy 2 naphthoate biosynthesis II |g__Staphylococcus.s__Staphylococcus_aureus\t8931.57710009\t1036.87621513\n+PWY0-1586\tpeptidoglycan maturation |g__Escherichia.s__Escherichia_coli\t18753.0219821\t2866.53948432\n+PWY-5181\ttoluene degradation III (via p cresol)\t947.6822035\t8800.26352918\n+PWY-5659\tGDP mannose biosynthesis|g__Escherichia.s__Escherichia_coli\t2998.91987725\t599.8717343\n+PWY-5861\tsuperpathway of demethylmenaquinol 8 biosynthesis|g__Escherichia.s__Escherichia_coli\t3430.13320251\t441.24808359\n+PWY-7220\tadenosine deoxyribonucleotides de novo biosynthesis II|g__Streptococcus.s__Streptococcus_mutans\t8808.69286571\t979.81451315\n+THISYNARA-PWY\tsuperpathway of thiamin diphosphate biosynthesis III |unclassified\t27.4597085\t4.34882378\n+PWY0-862\t dodec 5 enoate biosynthesis|g__Rhodobacter.s__Rhodobacter_sphaeroides\t15969.8171928\t2909.26805533\n+PWY-4242\tpantothenate and coenzyme A biosynthesis III|g__Streptococcus.s__Streptococcus_mutans\t1835.16841428\t1235.31350955\n+PWY-7389\tsuperpathway of anaerobic energy metabolism \t1843.01379918\t11881.3874654\n+SER-GLYSYN-PWY\tsuperpathway of L serine and glycine biosynthesis I|g__Escherichia.s__Escherichia_coli\t3369.37968613\t610.39579238\n+PWY-5138\tunsaturated, even numbered fatty acid β oxidation|g__Rhodobacter.s__Rhodobacter_sphaeroides\t11928.9247442\t3378.73427795\n+PWY-7388\toctanoyl [acyl carrier protein] biosynthesis |unclassified\t188.12545302\t274.49677967\n+PWY-724\tsuperpathway of L lysine, L threonine and L methionine biosynthesis II\t41547.2317349\t36974.2649936\n+PWY-5347\tsuperpathway of L methionine biosynthesis |g__Streptococcus.s__Streptococcus_mutans\t6303.81343752\t1187.03506311\n+POLYAMSYN-PWY\tsuperpathway of polyamine biosynthesis I|unclassified\t91.63013862\t13.26838762\n+PWY-5188\ttetrapyrrole biosynthesis I |g__Escherichia.s__Escherichia_coli\t3934.45905699\t738.40173753\n+DENITRIFICATION-PWY\tnitrate reduction I \t9285.14991359\t6301.73393977\n+HISDEG-PWY\tL histidine degradation I\t21504.3758787\t24267.6604905\n+PWY-6467\tKdo transfer to lipid IVA III |g__Escherichia.s__Escherichia_coli\t919.96428358\t332.28938386\n+PWY-5989\tstearate biosynthesis II |g__Staphylococcus.s__Staphylococcus_aureus\t6689.02064509\t1275.28632006\n+NONMEVIPP-PWY\tmethylerythritol phosphate pathway I\t21604.2127381\t41467.563069\n+PWY-6595\tsuperpathway of guanosine nucleotides degradation \t63659.5681895\t24658.3886983\n+PWY-7400\tL arginine biosynthesis IV \t59561.9426266\t54069.712201\n+PWY0-1061\tsuperpathway of L alanine biosynthesis|g__Clostridium.s__Clostridium_beijerinckii\t469.04005117\t1041.74348067\n+LEU-DEG2-PWY\tL leucine degradation I|g__Pseudomonas.s__Pseudomonas_aeruginosa\t292.84136182\t209.12320819\n+BIOTIN-BIOSYNTHESIS-PWY\tbiotin biosynthesis I\t38795.0783858\t31607.4904903\n+ARG+POLYAMINE-SYN\tsuperpathway of arginine and polyamine biosynthesis|g__Escherichia.s__Escherichia_coli\t3860.50746504\t701.87663984\n+PWY-5028\tL histidine degradation II\t7261.31861705\t8974.70796842\n+ASPASN-PWY\tsuperpathway of L aspartate and L asparagine biosynthesis|unclassified\t135.51257994\t180.94686582\n+HEME-BIOSYNTHESIS-II\theme biosynthesis I |g__Escherichia.s__Escherichia_coli\t4444.06370581\t1229.13243631\n+PWY-6565\tsuperpathway of polyamine biosynthesis III\t307.24774533\t5432.67232731\n+PWY-4221\tpantothenate and coenzyme A biosynthesis II \t6446.80589887\t3651.48403549\n+PWY-6282\tpalmitoleate biosynthesis I dodec 5 enoate)\t54100.9348987\t54847.3411852\n' |
| b |
| diff -r 9959fa526f1a -r c1aca37cb1fc test-data/similar_output.tabular --- a/test-data/similar_output.tabular Wed Apr 20 08:30:08 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,16 +0,0 @@ -id name sample1 sample2 -PWY-6897 thiamin salvage II|unclassified 3297150.0 0.909424 -PWY-1269 CMP 3 deoxy D manno octulosonate biosynthesis I 8260890.0 0.755658 -ARGININE-SYN4-PWY L ornithine de novo biosynthesis 35374100.0 0.809135 -HSERMETANA-PWY L methionine biosynthesis III|unclassified 15008900.0 0.515875 -PWY-6897 thiamin salvage II 3297150.0 0.415143 -PWY-7357 thiamin formation from pyrithiamine and oxythiamine 7205610.0 0.41402 -HSERMETANA-PWY L methionine biosynthesis III 15008900.0 1.21379 -DTDPRHAMSYN-PWY dTDP L rhamnose biosynthesis I|unclassified 14253800.0 2.50835 -PWY-7357 thiamin formation from pyrithiamine and oxythiamine |unclassified 7205610.0 0.906963 -ARGININE-SYN4-PWY L ornithine de novo biosynthesis|unclassified 35374100.0 1.66731 -PWY-6151 S adenosyl L methionine cycle I 6984130.0 0.977587 -PWY-1269 CMP 3 deoxy D manno octulosonate biosynthesis I|unclassified 8260890.0 0.644897 -KETOGLUCONMET-PWY ketogluconate metabolism 9615380.0 0.141222 -KETOGLUCONMET-PWY ketogluconate metabolism|unclassified 9615380.0 0.309365 -DTDPRHAMSYN-PWY dTDP L rhamnose biosynthesis I 14253800.0 1.69441 |
| b |
| diff -r 9959fa526f1a -r c1aca37cb1fc test-data/specific_to_sample1_output.txt --- a/test-data/specific_to_sample1_output.txt Wed Apr 20 08:30:08 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -id name abundances -PWY-6151 S adenosyl L methionine cycle I|unclassified 6984130.0 |
| b |
| diff -r 9959fa526f1a -r c1aca37cb1fc test-data/specific_to_sample2_output.txt --- a/test-data/specific_to_sample2_output.txt Wed Apr 20 08:30:08 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,252 +0,0 @@\n-id\tname\tabundances\n-PWY-6731\tstarch degradation III\t0.0336222\n-GLUDEG-I-PWY\tGABA shunt\t0.0537709\n-PWY-6123\tinosine 5 phosphate biosynthesis I\t0.831965\n-PWY-6769\trhamnogalacturonan type I degradation I |unclassified\t0.139081\n-PWY-6471\tpeptidoglycan biosynthesis IV \t0.0698193\n-PWY-7222\tguanosine deoxyribonucleotides de novo biosynthesis II\t1.48474\n-PPGPPMET-PWY\tppGpp biosynthesis\t0.203621\n-PWY-7234\tinosine 5 phosphate biosynthesis III\t0.045368\n-PWY-5686\tUMP biosynthesis|unclassified\t1.7892\n-PWY-3841\tfolate transformations II\t2.38544\n-P185-PWY\tformaldehyde assimilation III \t0.103843\n-ILEUSYN-PWY\tL isoleucine biosynthesis I \t1.29401\n-PWY-3001\tsuperpathway of L isoleucine biosynthesis I\t0.142024\n-PWY-5754\t4 hydroxybenzoate biosynthesis I |unclassified\t0.229464\n-PWY-6737\tstarch degradation V|unclassified\t0.316335\n-PWY-5104\tL isoleucine biosynthesis IV\t0.831272\n-PWY-7242\tD fructuronate degradation\t1.03935\n-OANTIGEN-PWY\tO antigen building blocks biosynthesis \t0.321981\n-PWY-5667\tCDP diacylglycerol biosynthesis I|unclassified\t0.149856\n-PWY-6606\tguanosine nucleotides degradation II|unclassified\t0.247734\n-PWY66-422\tD galactose degradation V |unclassified\t1.04266\n-PWY66-400\tglycolysis VI \t0.938218\n-PWY66-389\tphytol degradation\t0.548391\n-PWY-5097\tL lysine biosynthesis VI\t1.04893\n-1CMET2-PWY\tN10 formyl tetrahydrofolate biosynthesis|unclassified\t0.834716\n-PWY-6386\tUDP N acetylmuramoyl pentapeptide biosynthesis II \t0.0904748\n-PWY4LZ-257\tsuperpathway of fermentation \t0.147873\n-PWY-6549\tL glutamine biosynthesis III\t0.508899\n-GLCMANNANAUT-PWY\tsuperpathway of N acetylglucosamine, N acetylmannosamine and N acetylneuraminate degradation|unclassified\t0.123299\n-PWY-7111\tpyruvate fermentation to isobutanol |unclassified\t1.73067\n-PEPTIDOGLYCANSYN-PWY\tpeptidoglycan biosynthesis I \t0.850699\n-PWY-7115\tC4 photosynthetic carbon assimilation cycle, NAD ME type\t0.187881\n-P241-PWY\tcoenzyme B biosynthesis|unclassified\t0.0707035\n-PWY-6124\tinosine 5 phosphate biosynthesis II|unclassified\t2.22455\n-PWY-5173\tsuperpathway of acetyl CoA biosynthesis|unclassified\t0.0785602\n-PWY-7316\tdTDP N acetylviosamine biosynthesis\t0.542069\n-PWY-5101\tL isoleucine biosynthesis II|unclassified\t0.617859\n-PEPTIDOGLYCANSYN-PWY\tpeptidoglycan biosynthesis I |unclassified\t1.16221\n-PWY-6769\trhamnogalacturonan type I degradation I \t0.0634893\n-GLUCUROCAT-PWY\tsuperpathway of β D glucuronide and D glucuronate degradation\t0.838546\n-PWY-7219\tadenosine ribonucleotides de novo biosynthesis|unclassified\t3.33171\n-PWY4LZ-257\tsuperpathway of fermentation |unclassified\t0.318099\n-ARGSYN-PWY\tL arginine biosynthesis I \t1.16946\n-PWY-5100\tpyruvate fermentation to acetate and lactate II|unclassified\t1.26625\n-ARO-PWY\tchorismate biosynthesis I\t0.39449\n-ARGSYNBSUB-PWY\tL arginine biosynthesis II \t1.02161\n-PWY-6936\tseleno amino acid biosynthesis\t1.2799\n-PWY-6595\tsuperpathway of guanosine nucleotides degradation |unclassified\t0.225538\n-ANAGLYCOLYSIS-PWY\tglycolysis III \t1.03937\n-PWY0-162\tsuperpathway of pyrimidine ribonucleotides de novo biosynthesis|unclassified\t0.295685\n-PWY-841\tsuperpathway of purine nucleotides de novo biosynthesis I\t0.531622\n-PWY-5505\tL glutamate and L glutamine biosynthesis|g__Bacteroides.s__Bacteroides_thetaiotaomicron\t1.44739\n-THRESYN-PWY\tsuperpathway of L threonine biosynthesis|unclassified\t0.188356\n-PWY-5941\tglycogen degradation II \t0.127166\n-PWY-7094\tfatty acid salvage\t0.0597229\n-CITRULBIO-PWY\tL citrulline biosynthesis|unclassified\t0.49408\n-PWY-7221\tguanosine ribonucleotides de novo biosynthesis\t1.88123\n-ARGSYNBSUB-PWY\tL arginine biosynthesis II |unclassified\t1.31054\n-PWY-6630\tsuperpathway of L tyrosine biosynthesis\t0.319673\n-RIBOSYN2-PWY\tflavin biosynthesis I |unclassified\t0.213182\n-PWY-2942\tL lysine biosynthesis III|unclassified\t1.10762\n-PWY-7094\tfatty acid salvage|unclassified\t0.125407\n-PWY-1042\tglycolysis IV |unclassified\t1.93529\n-VALSYN-PWY\tL valine biosynthesis\t1.29401\n-PWY-6277\tsuperpathway of 5 aminoimidazole ribonucleotide biosynthesis|unclassified\t0.521078'..b'on\t0.88\n-THISYNARA-PWY\tsuperpathway of thiamin diphosphate biosynthesis III |unclassified\t0.21303\n-PWY-6123\tinosine 5 phosphate biosynthesis I|unclassified\t1.82252\n-PWY-6121\t5 aminoimidazole ribonucleotide biosynthesis I\t0.258418\n-COA-PWY-1\tcoenzyme A biosynthesis II \t1.9437\n-PWY-6936\tseleno amino acid biosynthesis|unclassified\t1.32349\n-PWY-6163\tchorismate biosynthesis from 3 dehydroquinate\t0.410329\n-PWY-5667\tCDP diacylglycerol biosynthesis I\t0.384585\n-PWY-7184\tpyrimidine deoxyribonucleotides de novo biosynthesis I\t0.770993\n-PWY-3841\tfolate transformations II|unclassified\t2.27477\n-CITRULBIO-PWY\tL citrulline biosynthesis\t0.974607\n-RHAMCAT-PWY\tL rhamnose degradation I\t0.539026\n-PWY-724\tsuperpathway of L lysine, L threonine and L methionine biosynthesis II|unclassified\t0.29625\n-GLUTORN-PWY\tL ornithine biosynthesis|unclassified\t0.900908\n-PWY-5265\tpeptidoglycan biosynthesis II |unclassified\t0.209837\n-PWY-5464\tsuperpathway of cytosolic glycolysis , pyruvate dehydrogenase and TCA cycle|unclassified\t0.172005\n-PWY-6606\tguanosine nucleotides degradation II\t0.113088\n-OANTIGEN-PWY\tO antigen building blocks biosynthesis |unclassified\t0.620846\n-PWY-7388\toctanoyl [acyl carrier protein] biosynthesis |unclassified\t0.641891\n-P185-PWY\tformaldehyde assimilation III |unclassified\t0.115303\n-METHGLYUT-PWY\tsuperpathway of methylglyoxal degradation\t0.226728\n-PWY-6737\tstarch degradation V\t0.201137\n-PWY-724\tsuperpathway of L lysine, L threonine and L methionine biosynthesis II\t0.142842\n-NONOXIPENT-PWY\tpentose phosphate pathway |unclassified\t1.8885\n-DAPLYSINESYN-PWY\tL lysine biosynthesis I\t0.35429\n-PWY-6628\tsuperpathway of L phenylalanine biosynthesis\t0.49241\n-THISYNARA-PWY\tsuperpathway of thiamin diphosphate biosynthesis III \t0.0973654\n-PWY-6385\tpeptidoglycan biosynthesis III \t0.820786\n-PWY1F-823\tleucopelargonidin and leucocyanidin biosynthesis\t0.0501896\n-ASPASN-PWY\tsuperpathway of L aspartate and L asparagine biosynthesis\t1.09751\n-P105-PWY\tTCA cycle IV |unclassified\t0.340536\n-TRNA-CHARGING-PWY\ttRNA charging|unclassified\t0.526713\n-GALACT-GLUCUROCAT-PWY\tsuperpathway of hexuronide and hexuronate degradation\t0.391566\n-PWY-5173\tsuperpathway of acetyl CoA biosynthesis\t0.0372086\n-FAO-PWY\tfatty acid β oxidation I\t0.0714249\n-P241-PWY\tcoenzyme B biosynthesis\t0.0322755\n-COMPLETE-ARO-PWY\tsuperpathway of aromatic amino acid biosynthesis|unclassified\t0.862669\n-HISDEG-PWY\tL histidine degradation I\t0.519408\n-COMPLETE-ARO-PWY\tsuperpathway of aromatic amino acid biosynthesis\t0.439273\n-DAPLYSINESYN-PWY\tL lysine biosynthesis I|unclassified\t0.314147\n-PWY-5103\tL isoleucine biosynthesis III\t0.831677\n-GLUDEG-I-PWY\tGABA shunt|unclassified\t0.1173\n-GLCMANNANAUT-PWY\tsuperpathway of N acetylglucosamine, N acetylmannosamine and N acetylneuraminate degradation\t0.0651572\n-P441-PWY\tsuperpathway of N acetylneuraminate degradation|unclassified\t0.204428\n-PWY-5686\tUMP biosynthesis\t0.980672\n-PWY-6595\tsuperpathway of guanosine nucleotides degradation \t0.102956\n-PWY66-422\tD galactose degradation V \t1.75745\n-PWY-5505\tL glutamate and L glutamine biosynthesis|unclassified\t1.96045\n-PWY-6305\tputrescine biosynthesis IV\t0.333385\n-HISDEG-PWY\tL histidine degradation I|unclassified\t0.770332\n-PWY-5659\tGDP mannose biosynthesis|unclassified\t0.106616\n-FAO-PWY\tfatty acid β oxidation I|unclassified\t0.148771\n-METHGLYUT-PWY\tsuperpathway of methylglyoxal degradation|unclassified\t0.496676\n-DENOVOPURINE2-PWY\tsuperpathway of purine nucleotides de novo biosynthesis II\t0.14462\n-PWY-5857\tubiquinol 10 biosynthesis \t0.15637\n-PWY-5101\tL isoleucine biosynthesis II\t0.492461\n-RIBOSYN2-PWY\tflavin biosynthesis I \t0.11474\n-SO4ASSIM-PWY\tsulfate reduction I |unclassified\t0.015138\n-BRANCHED-CHAIN-AA-SYN-PWY\tsuperpathway of branched amino acid biosynthesis\t1.02856\n-PWY-5265\tpeptidoglycan biosynthesis II \t0.106882\n-ASPASN-PWY\tsuperpathway of L aspartate and L asparagine biosynthesis|unclassified\t1.92205\n-PWY-7234\tinosine 5 phosphate biosynthesis III|unclassified\t0.0993843\n-GLYCOLYSIS\tglycolysis I |unclassified\t1.37456\n' |